VesselBasedDiscreteSource.cpp

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#include "VesselBasedDiscreteSource.hpp"
#include "AbstractCellPopulation.hpp"
#include "VesselNetwork.hpp"
#include "GeometryTools.hpp"
#include "Element.hpp"

template<unsigned DIM>
VesselBasedDiscreteSource<DIM>::VesselBasedDiscreteSource()
    :   DiscreteSource<DIM>(),
        mVesselPermeability(0.0*unit::metre_per_second),
        mReferenceConcentration(0.0*unit::mole_per_metre_cubed),
        mReferenceHaematocrit(1.0)
{

}

template<unsigned DIM>
VesselBasedDiscreteSource<DIM>::~VesselBasedDiscreteSource()
{

}

template<unsigned DIM>
boost::shared_ptr<VesselBasedDiscreteSource<DIM> > VesselBasedDiscreteSource<DIM>::Create()
{
    MAKE_PTR(VesselBasedDiscreteSource<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > VesselBasedDiscreteSource<DIM>::GetConstantInUMeshValues()
{
    if(!this->mpMesh)
    {
        EXCEPTION("A mesh is required for this type of source");
    }
    std::vector<units::quantity<unit::concentration_flow_rate> > values(this->mpMesh->GetNumElements(), 0.0*unit::mole_per_metre_cubed_per_second);
    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > element_segment_map = this->mpMesh->GetElementSegmentMap();

    for(unsigned idx=0; idx<element_segment_map.size(); idx++)
    {
        if(element_segment_map[idx].size()>0)
        {
            // Get the element nodal locations and element volume
            Element<DIM, DIM>* p_element = this->mpMesh->GetElement(idx);
            std::vector<DimensionalChastePoint<DIM> > element_vertices(4);
            double determinant = 0.0;
            c_matrix<double, DIM, DIM> jacobian;
            p_element->CalculateJacobian(jacobian, determinant);
            units::quantity<unit::volume> element_volume = p_element->GetVolume(determinant) * units::pow<3>(this->mpMesh->GetReferenceLengthScale());
            if(p_element->GetNumNodes() != 4)
            {
                EXCEPTION("Vessel mesh mapping only supported for linear tetrahedral elements.");
            }
            for (unsigned jdx = 0; jdx < 4; jdx++)
            {
                element_vertices[jdx] = DimensionalChastePoint<DIM>(p_element->GetNodeLocation(jdx), this->mpMesh->GetReferenceLengthScale());
            }

            for (unsigned jdx = 0; jdx < element_segment_map[idx].size(); jdx++)
            {

                units::quantity<unit::length> length_in_box = LengthOfLineInTetra<DIM>(element_segment_map[idx][jdx]->GetNode(0)->rGetLocation(),
                                                                element_segment_map[idx][jdx]->GetNode(1)->rGetLocation(), element_vertices);

                units::quantity<unit::area> surface_area = 2.0*M_PI*element_segment_map[idx][jdx]->GetRadius()*length_in_box;

                double haematocrit_Ratio = element_segment_map[idx][jdx]->GetFlowProperties()->GetHaematocrit()/mReferenceHaematocrit;
                values[idx] += mVesselPermeability * (surface_area/element_volume) * mReferenceConcentration * haematocrit_Ratio;
            }
        }
    }

    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > VesselBasedDiscreteSource<DIM>::GetLinearInUMeshValues()
{
    if(!this->mpMesh)
    {
        EXCEPTION("A mesh is required for this type of source");
    }
    std::vector<units::quantity<unit::rate> > values(this->mpMesh->GetNumElements(), 0.0*unit::per_second);
    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > element_segment_map = this->mpMesh->GetElementSegmentMap();

    for(unsigned idx=0; idx<element_segment_map.size(); idx++)
    {
        if(element_segment_map[idx].size()>0)
        {
            // Get the element nodal locations and element volume
            Element<DIM, DIM>* p_element = this->mpMesh->GetElement(idx);
            std::vector<DimensionalChastePoint<DIM> > element_vertices(4);
            double determinant = 0.0;
            c_matrix<double, DIM, DIM> jacobian;
            p_element->CalculateJacobian(jacobian, determinant);
            units::quantity<unit::volume> element_volume = p_element->GetVolume(determinant) * units::pow<3>(this->mpMesh->GetReferenceLengthScale());
            if(p_element->GetNumNodes() != 4)
            {
                EXCEPTION("Vessel mesh mapping only supported for linear tetrahedral elements.");
            }
            for (unsigned jdx = 0; jdx < 4; jdx++)
            {
                element_vertices[jdx] = DimensionalChastePoint<DIM>(p_element->GetNodeLocation(jdx), this->mpMesh->GetReferenceLengthScale());
            }

            for (unsigned jdx = 0; jdx < element_segment_map[idx].size(); jdx++)
            {
                units::quantity<unit::length> length_in_box = LengthOfLineInTetra<DIM>(element_segment_map[idx][jdx]->GetNode(0)->rGetLocation(),
                                                                element_segment_map[idx][jdx]->GetNode(1)->rGetLocation(), element_vertices);

                units::quantity<unit::area> surface_area = 2.0*M_PI*element_segment_map[idx][jdx]->GetRadius()*length_in_box;
                double haematocrit = element_segment_map[idx][jdx]->GetFlowProperties()->GetHaematocrit();
                if(haematocrit>0.0)
                {
                    values[idx] += mVesselPermeability * (surface_area/element_volume);
                }
            }
        }
    }

    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > VesselBasedDiscreteSource<DIM>::GetConstantInURegularGridValues()
{
    std::vector<units::quantity<unit::concentration_flow_rate> > values(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::mole_per_metre_cubed_per_second);
    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > point_segment_map = this->mpRegularGrid->GetPointSegmentMap();
    units::quantity<unit::length> grid_spacing = this->mpRegularGrid->GetSpacing();
    units::quantity<unit::volume> grid_volume = units::pow<3>(grid_spacing);
    for(unsigned idx=0; idx<point_segment_map.size(); idx++)
    {
        for (unsigned jdx = 0; jdx < point_segment_map[idx].size(); jdx++)
        {
            units::quantity<unit::length> length_in_box = LengthOfLineInBox<DIM>(point_segment_map[idx][jdx]->GetNode(0)->rGetLocation(),
                                                                         point_segment_map[idx][jdx]->GetNode(1)->rGetLocation(),
                                                                         this->mpRegularGrid->GetLocationOf1dIndex(idx), grid_spacing);

            units::quantity<unit::area> surface_area = 2.0*M_PI*point_segment_map[idx][jdx]->GetRadius()*length_in_box;

            double haematocrit_ratio = point_segment_map[idx][jdx]->GetFlowProperties()->GetHaematocrit()/mReferenceHaematocrit;
            values[idx] += mVesselPermeability * (surface_area/grid_volume) * mReferenceConcentration * haematocrit_ratio;
        }
    }
    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > VesselBasedDiscreteSource<DIM>::GetLinearInURegularGridValues()
{
    std::vector<units::quantity<unit::rate> > values(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::per_second);
    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > point_segment_map = this->mpRegularGrid->GetPointSegmentMap(false);
    units::quantity<unit::length> grid_spacing = this->mpRegularGrid->GetSpacing();
    units::quantity<unit::volume> grid_volume = units::pow<3>(grid_spacing);
    for(unsigned idx=0; idx<point_segment_map.size(); idx++)
    {
        for (unsigned jdx = 0; jdx < point_segment_map[idx].size(); jdx++)
        {
            units::quantity<unit::length> length_in_box = LengthOfLineInBox<DIM>(point_segment_map[idx][jdx]->GetNode(0)->rGetLocation(),
                                                                         point_segment_map[idx][jdx]->GetNode(1)->rGetLocation(),
                                                                         this->mpRegularGrid->GetLocationOf1dIndex(idx), grid_spacing);

            units::quantity<unit::area> surface_area = 2.0*M_PI*point_segment_map[idx][jdx]->GetRadius()*length_in_box;
            double haematocrit = point_segment_map[idx][jdx]->GetFlowProperties()->GetHaematocrit();
            if(haematocrit>0.0)
            {
                values[idx] -= mVesselPermeability * (surface_area/grid_volume);
            }
        }
    }
    return values;
}

template<unsigned DIM>
void VesselBasedDiscreteSource<DIM>::SetVesselPermeability(units::quantity<unit::membrane_permeability> value)
{
    mVesselPermeability = value;
}

template<unsigned DIM>
void VesselBasedDiscreteSource<DIM>::SetReferenceConcentration(units::quantity<unit::concentration> value)
{
    mReferenceConcentration = value;
}

template<unsigned DIM>
void VesselBasedDiscreteSource<DIM>::SetReferenceHaematocrit(units::quantity<unit::dimensionless> value)
{
    mReferenceHaematocrit = value;
}

// Explicit instantiation
template class VesselBasedDiscreteSource<2>;
template class VesselBasedDiscreteSource<3>;